old history interfering

Snakefile

@@ -99,9 +99,12 @@ else:
 #     return False
 #
 
+
+print("the number of threads to be used is", max_threads)
+
 if "Results" not in config:
         config["Results"] = "results"
-max_threads=workflow.cores
+
 report: "report/workflow.rst"
 
 include: "rules/rulesNew.smk"

rules/rulesNew.smk

@@ -228,12 +228,12 @@ rule merqury:
 				if wildcards.sample in samples.index else '',
 		merylDB=os.path.join(config['Results'],"{sample}"+ "/2_QVstats_merylAndMerqury/" + "{sample}" + "_dB.21.meryl")
 	params:
-		script = os.path.join(workflow.basedir, "programs/merqury_June2020/merqury.sh"),
+		script = os.path.join(workflow.basedir, "programs/merqury-1.1/merqury.sh"),
 		outFile= "{sample}" + "_merq",
 #		outFile= os.path.join(config['Results'], "{sample}" +"/QVstats_merylAndMerqury/{sample}_merq"),
 		merylPath = os.path.join(workflow.basedir, "programs/meryl-1.0/Linux-amd64/bin:$PATH"),
 		outPath= os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury"),
-		export= os.path.join(workflow.basedir, "programs/merqury_June2020")
+		export= os.path.join(workflow.basedir, "programs/merqury-1.1")
 		# symlink=os.path.join(config['Results'], "{sample}" + "/{sample}.fasta")
 	threads:
 		workflow.cores * 0.5
@@ -243,7 +243,7 @@ rule merqury:
 		report(os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.spectra-cn.fl.png"), caption="../report/merqury/spectra-cn_filled.rst", category="Copy Number Spectra Plots", subcategory="{sample}"),
 		os.path.join(config['Results'], "{sample}" +"/2_QVstats_merylAndMerqury/" + "{sample}" + "_dB.21.hist")
 	log:
-		os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/logs/" + "{sample}" + "_merq.spectra-cn.log")
+		os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/logs/{sample}_merqury.log")
 	priority:
 		3
 	conda:
@@ -268,7 +268,8 @@ rule merqury:
 rule genomescope2:
 	input:
 		hist=os.path.join(config['Results'], "{sample}" +"/2_QVstats_merylAndMerqury/" + "{sample}" + "_dB.21.hist"),
-		logCheck=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/logs/" + "{sample}" + "_merq.spectra-cn.log")
+		check1=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.spectra-cn.fl.png"),
+		check2=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.spectra-cn.st.png")
 	params:
 		outFolder=os.path.join(config['Results'], "{sample}" +"/3_genomescopeProfile/"),
 		cpHist=os.path.join(config['Results'], "{sample}" +"/3_genomescopeProfile/" + "{sample}" + "_dB.21.histo")
@@ -278,7 +279,7 @@ rule genomescope2:
 		linearPlot=report(os.path.join(config['Results'], "{sample}" +"/3_genomescopeProfile/" + "{sample}" + "_linear_plot.png"), caption="../report/genomescope/linearplot.rst", category="Genomescope Profile", subcategory="{sample}"),
 		estimatedSize=temp(os.path.join(config['Results'], "{sample}" +"/3_genomescopeProfile/" + "{sample}" + "_sizeEst.txt"))
 	conda:
-		"../envs/merylMerq.yaml"
+		"../envs/genomescope.yaml"
 	shell:
 		"""
 		expand -t 1 {input.hist} > {params.cpHist}
@@ -340,7 +341,7 @@ rule assemblyStats:
 
 rule saveConfiguration_and_getKeyValues:
 	input:
-		checkLog=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/logs/" + "{sample}" + "_merq.spectra-cn.log"),
+#		checkLog=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/logs/" + "{sample}" + "_merq.spectra-cn.log"),
 		gscopeSum=os.path.join(config['Results'], "{sample}" +"/3_genomescopeProfile/" + "{sample}" + "_summary.txt"),
 		gscopeLog=os.path.join(config['Results'], "{sample}" +"/3_genomescopeProfile/" + "{sample}" + "_log_plot.png"),
 		gscopeLin=os.path.join(config['Results'], "{sample}" +"/3_genomescopeProfile/" + "{sample}" + "_linear_plot.png"),
@@ -362,7 +363,7 @@ rule saveConfiguration_and_getKeyValues:
 	output:
 		# newSampleSheet=os.path.join(config['Results'],"{sample}"+ "/keyResults/savedSampleSheet.tsv"),
 		# newConfigFile=os.path.join(config['Results'],"{sample}"+ "/keyResults/savedConfig.yaml"),
-		merqLog=os.path.join(config['Results'],"logs/2_merylAndMerq/" + "{sample}" + "_merqury.spectra-cn.log"),
+#		merqLog=os.path.join(config['Results'],"logs/2_merylAndMerq/" + "{sample}" + "_merqury.spectra-cn.log"),
 		keyValues=temp(os.path.join(config['Results'],"{sample}"+ "/5_Key_Results/aggregate.tsv")),
 		rowNames=temp(os.path.join(config['Results'],"{sample}"+ "/5_Key_Results/aggregate_rowNames.tsv")),
 		keyValuesWithRowNames=os.path.join(config['Results'],"{sample}"+ "/5_Key_Results/{sample}_aggregatedResults.tsv"),
@@ -384,7 +385,6 @@ rule saveConfiguration_and_getKeyValues:
 		"../envs/dos2unix.yaml"
 	shell:
 		"""
-		cp {input.checkLog} {output.merqLog}
 		cp {input.gscopeSum} {output.gscopeSum}
 		cp {input.gscopeLog} {output.gscopeLog}
 		cp {input.gscopeLin} {output.gscopeLin}